Avira, the amount of amaratzus in your latest (long) post is simply astounding. How are you able to make such ridiculous statements with such confidence?
In the sugya in Sanhedrin, I counted no fewer than five Tannoim and Amoroim who prove תחית המתים מן התורה from a פסוק in נ”ך. The term תורה in this context refers to the entirety of תנ”ך. Rashi cannot be referring to a particular דרשה, as you mistakenly imagine; he says, “שכופר במדרשים דדרשינן בגמרא לקמן מניין לתחיית המתים מן התורה.” (For your information, the word מדרשים is a plural.)
When the Radak says a non-Halachic interpretation of חז”ל is דברים של תימה, he is rejecting their פשט. This is entirely unlike תוספות, which asks a קשיא, and then (9 times out of 10) continues to a תירוץ.
I know Rabbeinu Saadiah Gaon’s פירוש was written in Arabic. Not sure what you want from that. There is no reason to assume it’s unreliable. Regardless, he is certainly referring to Rebbi Yochanan, as he even brings R’ Yochanan’s proof text – the פסוק in יחזקאל. (See the מגיה for further confirmation that this is his meaning.) R’ Shmuel Motot’s פשט doesn’t hold much water (pun intended): he learns that according to R’ Yochanan it did not rain in Eretz Yisroel, but the water which rained on other lands flowed into Eretz Yisroel. If so, the whole Gemoro in Zevochim makes no sense. For example, Rebbi Yochanan understands the word בחרבה as a reference to Eretz Yisroel STAYING DRY during the flood. He also says that the people in Eretz Yisroel died from heat, not the floodwaters.
You then move on to Rebbi Yochanan’s encounter with the kusi. Now, as far as I know this Medrash appears in four places: Breishis Rabbah, Shir haShirim Rabbah, Devorim Rabbah and Yalkut Shimoni. In all four places the name of the אמורא is רבי יונתן. I know this may come as a surprise, but Rebbi Yochanan and Rebbi Yonasan were two different people! (Tosafos in Zevochim 113a s.v. lo has the story happening to Rebbi Yishmael beRebbi Yosi, who was also a different person.)
I’m not sure why the Abarbanel goes to such lengths to explain how the Ramban can fit with Chazal. Maybe he was scared that if people saw the Ramban rejecting one Chazal about Moshiach, they would feel free to reject others. But it is undeniable the the Abarbanel himself often disagrees with Chazal. In that very same chapter (Melochim I 10) he brings the words of Chazal that מלכת שבא wasn’t a queen but a kingdom, and rejects them, saying ואין לנו לזוז מפשט הכתוב.
The Rambam did not need to bring any examples of מכחיש מגידיה; the fact he does so proves he is only referring to people like צדוק ובייתוס, and not people who only reject Chazal’s non-Halachic droshos. Denying Olam Habo is a serious matter, and falls within Chazal’s remit. I accept Chazal’s religious authority (and so their ability to codify articles of faith), just not their scientific authority, even when based on droshos.
The quotation from Rav Shmuel bar Chofni Gaon is still in the same place it was on Sunday: in the Radak to Shmuel Alef 28, 24.